A classic at my high school was taking a screen shot of the desktop with icons, setting it as the desktop background, then hiding all the desktop icons.
Bonus points if you could get the teachers machine
I rotated the screenshot to be upside down, set it as a background and then rotated the whole screen on Display settings. So that the background would be on the correct orientation but the mouse cursor and everything would be reversed.
The favorite prank played on me was coworkers changing my wallpaper to a "funny" picture, then renaming *.jpg to *.old and replacing the original *.jpg's with the same "funny" picture. So when I went to change my wallpaper back, it seemed like it didn't work. Harmless (mv *.old *.jpg, slightly more complicated, obviously) and funny!
Good times :D